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Table 3 Time and percentage of pairs processed for each method and dataset

From: Fast phylogenetic inference from typing data

Dataset

k

Naïve

Binary search

LCP clusters

t (s)

Pairs (%)

t (s)

Pairs (%)

t (s)

Pairs (%)

C. jejuni

8

108.59

100

0.22

0.06

0.17

0.06

 

16

109.30

100

0.48

0.32

0.34

0.32

 

32

108.60

100

3.52

5.45

2.67

5.45

 

64

108.60

100

231.05

99.98

162.36

99.98

S. enterica

8

89.85

100

1.04

2.37

0.95

2.37

 

16

87.26

100

7.16

12.69

6.73

12.69

 

32

85.36

100

36.29

33.22

30.76

33.22

 

64

84.63

100

254.45

82.44

187.15

82.44

S. typhi

89

28.83

100

16.63

91.48

12.02

91.48

 

178

28.32

100

46.98

99.91

32.03

99.91

 

890

30.04

100

113.57

100

129.14

100

S. pneumoniae

8

0.56

100

0.02

0.93

0.02

0.93

 

16

0.57

100

0.05

1.71

0.04

1.71

 

32

0.56

100

0.20

4.42

0.15

4.42

 

64

0.58

100

5.63

73.36

5.01

73.36

  1. The minimum time for each row is highlighted in italic